source: extensions/net.sf.basedb.mev/trunk/README @ 1294

Last change on this file since 1294 was 1294, checked in by Nicklas Nordborg, 12 years ago

Fixes #279: Plug-in should suggest better job names

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[666]1== Requirements ==
2
[1294]3 1. BASE 2.17.0 or later.
[666]4 
5== Introduction ==
6
7This package is an extension package to BASE that installs an action that
8opens TIGR MultiExperiment Viewer (MEV) as a Java webstart application and
9automatically imports data from the currently selected bioassay set. This
[1228]10extension uses the standard MEV 4.6.1 distribution that has been
[976]11Java Webstart enabled. For more information:
[666]12
13 * The homepage for this extension:
14   http://baseplugins.thep.lu.se/wiki/net.sf.basedb.mev
15 * The official MEV homepage: http://www.tm4.org/mev.html
16
17== Installation ==
18
[690]19 1. Download the mev-launcher-*.tar.gz file.
[666]20 2. Unpack the downloaded file to a directory of your choice.
21 3. Copy the mev-launcher.jar file to your BASE extensions directory:
22    WEB-INF/extensions.
23 4. Run the 'Extensions -> Manual scan' command if you have disabled automatic
24    installation. Otherwise, just wait a bit and the automatic installation will
[690]25    find and install the new extension.
[1068]26 5. Run the plug-in installation wizard by clicking the 'New' button on the
[1082]27    'Administrate -> Plugins -> Definitions' page. Make sure the option for
[1068]28    the 'Extensions directory' is selected. Install all plug-ins found in
29    the mev-launcher.jar file.
[1159]30 6. Run the 'MeV package installer' plug-in. Find this plug-in on the
31    'Administrate -> Plugins -> Definitions' page, click on it, and then
32    on the 'Run plugin' button. Complete the installation wizard. This will
33    install required items, eg. data file types, that are required by MeV.
34 7. The 'MeV CGH exporter' plug-in requires that an admin configures the
35    reporter annotations that corresponds to the CGH file columns. Go to the
[1082]36    'Administrate -> Plugins -> Definitions' page and click on the
[1099]37    'MeV CGH exporter' plug-in. Click on 'New configuration...' and
[1082]38    enter a name and optionally a description. Then, click on 'Save and
39    configure' and select the corresponding reporter annotation columns
40    for the four CGH file columns (chromosome, start, end and description).
[1159]41    Finish the configuration.
[1182]42 8. Share the TDMS and CGH exporter plug-ins, including the configuration
43    that you created in the previous step, plug-ins to the desired
44    users and/or groups. Otherwise, only the root user and administrators
45    can use MeV.
46 9. Done.
[1068]47 
48 The MeV Launcher appears as an action in the "Tools" column when
49 viewing bioassay sets of an experiment. Some (per-user) options can be
50 specified by opening the 'Extensions -> MeV Launcher options' menu.
[666]51
[1068]52The MeV export plug-ins appears in the 'Export' dialog when viewing
53bioassay sets of an experiment.
54
[666]55== Known issues ==
56
[1190]57MeV modules that use R will not work. See the "Known issues" section
58at http://www.tm4.org/mev/features/releases for more information.
[666]59
60== Compiling ==
61
62To compile this package you also need:
63 
64 1. Ant 1.6
65 2. Java 1.6
66
67Follow these instructions:
68
69 1. Download the source code from the subversion repository. See
70    http://baseplugins.thep.lu.se/wiki/net.sf.basedb.mev for instructions.
71 
[1191]72 2. Type `ant download-lib` to automatically download the BASE core JAR files that
[690]73    are neeed for compilation. You can also do this manually by copying the
[976]74    BASE2Core.jar, BASE2Webclient.jar, BASE2CorePlugins.jar and BASE2WSClient.jar
[974]75    from the BASE installation directory (<basedir>/www/WEB-INF/lib/) to the
[666]76    ./lib/compile directory.
77
78 3. Type 'ant' to compile the code and generate the 'mev-launcher.jar' file
79    in the project directory.
80
81 4. Use 'ant package' to create a downloadable tar.gz package.
[690]82 
83Tip: If you need different values for any of the properties defined in
84the 'build.xml' file, create a file named 'build.properties' and set
85the values there.
[976]86
87Note! If upgrading MeV to a new version, the new JAR files needs to
88be signed. See `./jarsign/readme.txt` for more information.
89
90
91== Contributions ==
92
93 * David Waring, for helping out with MeV 4.3 integration.
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